*/
package jalview.schemes;
+import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
+import jalview.analysis.scoremodels.ScoreModels;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
public Color findColour(char res, int j, SequenceI seq,
String consensusResidue, float pid)
{
+ PairwiseSeqScoreModel sm = (PairwiseSeqScoreModel) ScoreModels
+ .getInstance().forName(ScoreModels.BLOSUM62);
+
/*
* compare as upper case; note consensusResidue is
* always computed as uppercase
for (char consensus : consensusResidue.toCharArray())
{
- score += ResidueProperties.getBLOSUM62(consensus, res);
+ score += sm.getPairwiseScore(consensus, res);
+ // score += ResidueProperties.getBLOSUM62(consensus, res);
}
if (score > 0)